Small fixes and updated doc.

CMakeLists.txt

@@ -78,7 +78,7 @@ if(NOT DISABLE_DOCUMENTATION)
   find_package(Sphinx ${PYTHON_VERSION} REQUIRED)
   set(PYTHON_DOC_URL "https://docs.python.org/${PYTHON_VERSION}")
   # set this to the URL corresponding to the version of OST you are using
-  set(OST_DOC_URL "http://www.openstructure.org/docs/1.3")
+  set(OST_DOC_URL "http://www.openstructure.org/docs/1.5")
 endif()
 find_package(OPENSTRUCTURE 1.4 REQUIRED 
              COMPONENTS io mol seq seq_alg mol_alg conop)

modelling/pymod/_closegaps.py

@@ -1251,9 +1251,8 @@ def CloseLargeDeletions(mhandle, scorer, structure_db, linker_length=8,
         
 
 # these methods will be exported into module
-__all__ = ('SetupBackboneScorer', 'CloseSmallDeletions', 'MergeGapsByDistance',
-           'FillLoopsByDatabase', 'FillLoopsByMonteCarlo', 'ModelTermini',
-           'CloseLargeDeletions')
+__all__ = ('CloseSmallDeletions', 'MergeGapsByDistance', 'FillLoopsByDatabase',
+           'FillLoopsByMonteCarlo', 'ModelTermini', 'CloseLargeDeletions')
 
 #  LocalWords:  modeling stereochemically param idx init
 #  LocalWords:  py ost pylint modelling promod CloseSmallDeletions

modelling/pymod/_molprobity.py

@@ -33,7 +33,7 @@ def RunMolProbity(target_pdb, molprobity_bin=None):
              - "Ramachandran outliers" (percentage [0,100] as :class:`float`)
              - "Ramachandran favored" (percentage [0,100] as :class:`float`)
              - "Rotamer outliers" (percentage [0,100] as :class:`float`)
-             - "C-beta deviations" (:class:`integer`)
+             - "C-beta deviations" (:class:`int`)
              - "Clashscore" (:class:`float`)
              - "MolProbity score" (:class:`float`)
              - "RMS(bonds)" (:class:`float`)

modelling/pymod/_pipeline.py

@@ -271,7 +271,7 @@ def MinimizeModelEnergy(mhandle, max_iterations=12, max_iter_sd=20,
 
     :param extra_force_fields: Additional list of force fields to use (see
                                :meth:`BuildFromRawModel`).
-    :type extra_force_fields:  :class:`list` of :class:`ost.mol.Forcefield`
+    :type extra_force_fields:  :class:`list` of :class:`ost.mol.mm.Forcefield`
 
     :return: The model including all oxygens as used in the minimizer.
     :rtype:  :class:`Entity <ost.mol.EntityHandle>`
@@ -433,7 +433,7 @@ def BuildFromRawModel(mhandle, scorer = None, use_amber_ff=False, extra_force_fi
                                default force field. The force fields are tried
                                in the order as given and ligands without an
                                existing parametrization are skipped.
-    :type extra_force_fields:  :class:`list` of :class:`ost.mol.Forcefield`
+    :type extra_force_fields:  :class:`list` of :class:`ost.mol.mm.Forcefield`
 
     :return: Delivers the model as an |ost_s| entity.
     :rtype: :class:`Entity <ost.mol.EntityHandle>`